Research workbench
Crystal structure of a binding protein component of ABC phosphonate transporter (PA3383) from pseudomonas aeruginosa at 1.97 a resolution
Analyse Crystal structure of a binding protein component of ABC phosphonate transporter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N5L
- Type
- protein
- Length
- 608 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Binding protein component of ABC phosphonate transporter
- UniProt
- Q9HYL8
- Ligands
- UNL, SO4, CL
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Binding protein component of ABC phosphonate transporter | protein | 306 | 52% helix, 22% strand | Q9HYL8 |
| B | Binding protein component of ABC phosphonate transporter | protein | 302 | 52% helix, 22% strand | Q9HYL8 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 22 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.77 | 0.97 | 34 | UNL |
| 2 | 104 | 0.76 | 0.96 | 29 | UNL |
| 3 | 645 | 0.76 | 0.82 | 74 | EDO |
| 4 | 141 | 0.40 | 0.74 | 23 | SO4 |
| 5 | 73 | 0.38 | 0.78 | 15 | EDO |
Interfaces
1 interface between chains.
- A–B · 895 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3N5L · Crystal structure of a binding protein component of ABC phosphonate transporter (PA3383)… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9HYL8
- Elsewhere: RCSB PDB 3N5L · PDBe 3N5L · UniProt Q9HYL8
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